人口统计学和罕见变异的年龄
Demography and the age of rare variants
摘要：
大型全基因组测序项目提供了对人类群体中许多罕见变异的访问，这对人口结构和最近的人口统计学具有高度的信息性。在这里，我们展示了如何从单倍型共享模式中估计罕见变异的年龄，以及这些年龄如何与种群之间的历史关系相关。我们调查了由1000个基因组计划测序的全球样本中恰好发生两次（f2变体）的变体的年龄分布，揭示了不同人群之间的巨大差异。携带f2变异的单倍型的中位年龄在欧洲或亚洲人群中为50至160代，在非洲为170至320代。各大洲之间共享的单倍型要古老得多，欧洲和亚洲之间共享的单倍型的中位年龄从320代到670代不等。f2单倍型的年龄分布是关于其人口统计学的信息，揭示了最近的瓶颈，古老的分裂和更现代的人口之间的联系。我们在观察中看到了选择的特征，即功能性变体明显比相同频率的非功能性变体年轻。这种方法对突变率相对不敏感，并且补充了用于人口统计推断的其他非参数方法。
英文摘要：
Large whole-genome sequencing projects have provided access to much of the rare variation in human populations, which is highly informative about population structure and recent demography. Here, we show how the age of rare variants can be estimated from patterns of haplotype sharing and how these ages can be related to historical relationships between populations. We investigate the distribution of the age of variants occurring exactly twice (f2 variants) in a worldwide sample sequenced by the 1000 Genomes Project, revealing enormous variation across populations. The median age of haplotypes carrying f2 variants is 50 to 160 generations across populations within Europe or Asia, and 170 to 320 generations within Africa. Haplotypes shared between continents are much older with median ages for haplotypes shared between Europe and Asia ranging from 320 to 670 generations. The distribution of the ages of f2 haplotypes is informative about their demography, revealing recent bottlenecks, ancient splits, and more modern connections between populations. We see the signature of selection in the observation that functional variants are significantly younger than nonfunctional variants of the same frequency. This approach is relatively insensitive to mutation rate and complements other nonparametric methods for demographic inference.
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